Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this
to extract flanking regions for cloning. If the result of the multiple sequence alignment is
not as expected, these results could be used for further investigation.
qseqid
sseqid
percentage.identical
alignment.length
no.mismatch
no.gap.openings
qstart
qend
sstart
send
evalue
bitscore
0
TraesCS6B01G129800
chr6B
100.000
4908
0
0
1
4908
126216882
126221789
0.000000e+00
9064.0
1
TraesCS6B01G129800
chr6B
89.452
1441
143
8
1886
3323
126629833
126631267
0.000000e+00
1810.0
2
TraesCS6B01G129800
chr6B
90.538
539
48
2
1
536
41378377
41378915
0.000000e+00
710.0
3
TraesCS6B01G129800
chr6B
82.511
223
23
6
1685
1891
449292723
449292501
1.090000e-41
182.0
4
TraesCS6B01G129800
chr6D
95.451
2374
71
19
2043
4411
56020647
56022988
0.000000e+00
3751.0
5
TraesCS6B01G129800
chr6D
88.843
1452
144
13
1886
3326
56275357
56276801
0.000000e+00
1768.0
6
TraesCS6B01G129800
chr6D
88.630
1029
61
19
609
1603
56019214
56020220
0.000000e+00
1201.0
7
TraesCS6B01G129800
chr6D
89.514
391
31
2
2865
3245
62244002
62243612
2.050000e-133
486.0
8
TraesCS6B01G129800
chr6D
88.591
298
14
4
1607
1884
56020251
56020548
1.310000e-90
344.0
9
TraesCS6B01G129800
chr6D
76.140
570
76
35
710
1236
56273980
56274532
1.360000e-60
244.0
10
TraesCS6B01G129800
chr6A
94.428
2315
79
19
1889
4184
70571016
70573299
0.000000e+00
3515.0
11
TraesCS6B01G129800
chr6A
90.110
1365
122
11
1972
3326
70911812
70913173
0.000000e+00
1760.0
12
TraesCS6B01G129800
chr6A
91.017
1013
69
10
609
1603
70569457
70570465
0.000000e+00
1347.0
13
TraesCS6B01G129800
chr6A
87.708
301
11
10
1607
1883
70570503
70570801
1.320000e-85
327.0
14
TraesCS6B01G129800
chr6A
94.737
95
3
1
4191
4285
70574657
70574749
3.960000e-31
147.0
15
TraesCS6B01G129800
chr6A
98.718
78
1
0
4334
4411
70574751
70574828
6.620000e-29
139.0
16
TraesCS6B01G129800
chr6A
86.275
102
10
3
4808
4908
112606472
112606374
1.870000e-19
108.0
17
TraesCS6B01G129800
chr7B
98.512
605
7
1
1
603
693836993
693836389
0.000000e+00
1066.0
18
TraesCS6B01G129800
chr7B
96.640
506
10
1
4410
4908
41518534
41519039
0.000000e+00
833.0
19
TraesCS6B01G129800
chr2B
98.512
605
7
1
1
603
194644427
194643823
0.000000e+00
1066.0
20
TraesCS6B01G129800
chr2B
89.312
683
54
8
2648
3320
23365379
23366052
0.000000e+00
839.0
21
TraesCS6B01G129800
chr2B
95.059
506
15
3
4411
4908
462919953
462920456
0.000000e+00
787.0
22
TraesCS6B01G129800
chr2B
94.702
151
7
1
4411
4560
462919753
462919903
2.950000e-57
233.0
23
TraesCS6B01G129800
chr5B
96.812
596
15
3
1
593
271040433
271041027
0.000000e+00
992.0
24
TraesCS6B01G129800
chr4D
95.586
589
24
1
1
587
497421055
497421643
0.000000e+00
942.0
25
TraesCS6B01G129800
chr4D
95.676
555
22
1
1
553
497414089
497414643
0.000000e+00
891.0
26
TraesCS6B01G129800
chr4D
90.492
589
30
7
1
587
497438167
497438731
0.000000e+00
754.0
27
TraesCS6B01G129800
chr4D
90.186
591
29
5
1
587
497417633
497418198
0.000000e+00
743.0
28
TraesCS6B01G129800
chr4D
90.039
512
26
2
1
510
497424657
497425145
1.490000e-179
640.0
29
TraesCS6B01G129800
chr2D
89.286
588
38
6
1
586
618134304
618134868
0.000000e+00
713.0
30
TraesCS6B01G129800
chr2D
85.897
156
18
3
4753
4908
469887768
469887919
3.930000e-36
163.0
31
TraesCS6B01G129800
chr3B
90.891
505
33
7
4413
4908
222141505
222142005
0.000000e+00
665.0
32
TraesCS6B01G129800
chr3B
86.922
497
32
16
4414
4908
790740828
790741293
1.210000e-145
527.0
33
TraesCS6B01G129800
chr5A
86.907
443
31
15
1889
2330
121943023
121942607
5.750000e-129
472.0
34
TraesCS6B01G129800
chr5A
86.682
443
29
17
1889
2330
123291790
123291377
9.620000e-127
464.0
35
TraesCS6B01G129800
chr5A
85.779
443
37
17
1889
2330
519494577
519494160
3.490000e-121
446.0
36
TraesCS6B01G129800
chr5A
83.908
174
12
1
1734
1891
121943259
121943086
8.510000e-33
152.0
37
TraesCS6B01G129800
chr5A
83.908
174
12
1
1734
1891
123292026
123291853
8.510000e-33
152.0
38
TraesCS6B01G129800
chr5A
93.617
47
1
2
1843
1887
490406473
490406427
8.820000e-08
69.4
39
TraesCS6B01G129800
chr2A
89.628
376
30
2
2865
3232
659628980
659628606
2.070000e-128
470.0
40
TraesCS6B01G129800
chr2A
88.747
391
34
2
2865
3245
735655915
735655525
2.070000e-128
470.0
41
TraesCS6B01G129800
chr7D
90.785
293
22
5
2049
2339
19643191
19643480
2.140000e-103
387.0
42
TraesCS6B01G129800
chr1B
91.829
257
18
2
4652
4908
581700874
581700621
6.040000e-94
355.0
43
TraesCS6B01G129800
chr1B
84.400
250
22
8
4568
4802
389317221
389316974
3.820000e-56
230.0
44
TraesCS6B01G129800
chr1D
79.562
411
57
13
4411
4797
287618658
287618251
8.100000e-68
268.0
45
TraesCS6B01G129800
chr4B
80.172
232
20
11
1677
1891
592868612
592868390
3.060000e-32
150.0
46
TraesCS6B01G129800
chr3A
91.489
47
2
2
1843
1887
148996326
148996280
4.100000e-06
63.9
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the
BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are
purely upstream or downstream may be removed if they don't overlap both primers.
query
scaffold
start
end
length
rev.comp
avg.bitscore
max.bitscore
avg.percent.identical
query.start
query.end
num_hsp
groupid
homo_length
0
TraesCS6B01G129800
chr6B
126216882
126221789
4907
False
9064.000000
9064
100.000000
1
4908
1
chr6B.!!$F2
4907
1
TraesCS6B01G129800
chr6B
126629833
126631267
1434
False
1810.000000
1810
89.452000
1886
3323
1
chr6B.!!$F3
1437
2
TraesCS6B01G129800
chr6B
41378377
41378915
538
False
710.000000
710
90.538000
1
536
1
chr6B.!!$F1
535
3
TraesCS6B01G129800
chr6D
56019214
56022988
3774
False
1765.333333
3751
90.890667
609
4411
3
chr6D.!!$F1
3802
4
TraesCS6B01G129800
chr6D
56273980
56276801
2821
False
1006.000000
1768
82.491500
710
3326
2
chr6D.!!$F2
2616
5
TraesCS6B01G129800
chr6A
70911812
70913173
1361
False
1760.000000
1760
90.110000
1972
3326
1
chr6A.!!$F1
1354
6
TraesCS6B01G129800
chr6A
70569457
70574828
5371
False
1095.000000
3515
93.321600
609
4411
5
chr6A.!!$F2
3802
7
TraesCS6B01G129800
chr7B
693836389
693836993
604
True
1066.000000
1066
98.512000
1
603
1
chr7B.!!$R1
602
8
TraesCS6B01G129800
chr7B
41518534
41519039
505
False
833.000000
833
96.640000
4410
4908
1
chr7B.!!$F1
498
9
TraesCS6B01G129800
chr2B
194643823
194644427
604
True
1066.000000
1066
98.512000
1
603
1
chr2B.!!$R1
602
10
TraesCS6B01G129800
chr2B
23365379
23366052
673
False
839.000000
839
89.312000
2648
3320
1
chr2B.!!$F1
672
11
TraesCS6B01G129800
chr2B
462919753
462920456
703
False
510.000000
787
94.880500
4411
4908
2
chr2B.!!$F2
497
12
TraesCS6B01G129800
chr5B
271040433
271041027
594
False
992.000000
992
96.812000
1
593
1
chr5B.!!$F1
592
13
TraesCS6B01G129800
chr4D
497414089
497425145
11056
False
804.000000
942
92.871750
1
587
4
chr4D.!!$F2
586
14
TraesCS6B01G129800
chr4D
497438167
497438731
564
False
754.000000
754
90.492000
1
587
1
chr4D.!!$F1
586
15
TraesCS6B01G129800
chr2D
618134304
618134868
564
False
713.000000
713
89.286000
1
586
1
chr2D.!!$F2
585
16
TraesCS6B01G129800
chr3B
222141505
222142005
500
False
665.000000
665
90.891000
4413
4908
1
chr3B.!!$F1
495
17
TraesCS6B01G129800
chr5A
121942607
121943259
652
True
312.000000
472
85.407500
1734
2330
2
chr5A.!!$R3
596
18
TraesCS6B01G129800
chr5A
123291377
123292026
649
True
308.000000
464
85.295000
1734
2330
2
chr5A.!!$R4
596
AutoCloner calculated primer pairs
These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3),
whilst remaining within the specified product range where possible.
Listed here are all possible primers based on the multiple sequence alignment and SNPs generated
previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work
during PCR or sequencing,
these could be used as alternatives.